Add VAT validation rule #2 [VS-19]

[RoriCremer]

Unlike the other validation rules, this does not test the validity of the VAT, but whether the pipeline completed as we expected it to--so I have added this as the singular test that runs during the pipeline.

Validation Rule 2: The number of passing variants in GVS matches the number of variants in the VAT. Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task.

Another way to phrase it: "If I were to make a sites only VCF of GVS and split each passing variant into it's own line, that number should equal the number of unique VIDs in the VAT."

Measure number of unique variants in sites only VCF that is generated.

We don't want to count filtered variants so we can't count the GVS table.

NOTE:

this pr also has some general cleanup as per discussion with Andrea.
where would y'all suggest I put the template file for the custom annotations?

[ahaessly]

I'm not sure where to put the template. maybe in a google bucket?
another option is that we could inline it in the wdl.

otherwise 👍